info.bioinfweb.libralign.model.implementations

Class AbstractListAlignmentModel<T>

java.lang.Object

info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel<T>

info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel<T>

info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel<java.util.List<T>,T>

info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel<T>

Type Parameters:

T - the type of sequence elements (tokens) the implementing provider object works with

All Implemented Interfaces:

AlignmentModel<T>

Direct Known Subclasses:

ArrayListAlignmentModel, PackedAlignmentModel

public abstract class AbstractListAlignmentModel<T>
extends AbstractMapBasedAlignmentModel<java.util.List<T>,T>

An abstract implementation of AlignmentModel using a map of lists to store alignment data.

Since:

0.1.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_INITIAL_CAPACITY

Constructor Summary

Constructors

Constructor and Description
AbstractListAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs) Creates a new instance of this class using DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.
AbstractListAlignmentModel(TokenSet<T> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs, int initialCapacity, boolean useMaxLength) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected java.util.List<T>	createNewSequence(java.lang.String sequenceID, java.lang.String sequenceName) Implementing classes must offer a way to create their custom instances of sequence objects overwriting this method.
protected abstract java.util.List<T>	createNewSequence(java.lang.String sequenceID, java.lang.String sequenceName, int initialCapacity) This method is called by #createNewSequence(int, String) and must be implemented by inherited classes.
int	getInitialCapacity() Returns the default initial capacity of new list objects created by #createNewSequence(int, String, int).
java.util.List<T>	getSequence(java.lang.String sequenceID)
int	getSequenceLength(java.lang.String sequenceID) Returns the length of the specified sequence.
T	getTokenAt(java.lang.String sequenceID, int index) Returns the token at the specified position.
AlignmentModelWriteType	getWriteType() Returns a value that specifies if whole sequences or single tokens can be edited in the underlying data source.
void	insertTokenAt(java.lang.String sequenceID, int index, T token) Inserts a token at the specified position.
void	insertTokensAt(java.lang.String sequenceID, int beginIndex, java.util.Collection<? extends T> tokens) Inserts a sequence of tokens starting at the specified position.
boolean	isUseMaxLength() Determines if the initial capacity of newly generated list objects shall only depend on the default capacity or also on the maximum length of the other lists already contained in this provider.
void	removeTokenAt(java.lang.String sequenceID, int index) Removes the token at the specified position from the underlying data source.
void	removeTokensAt(java.lang.String sequenceID, int beginIndex, int endIndex) Removes the token inside the specified interval from the underlying data source.
void	setTokenAt(java.lang.String sequenceID, int index, T token) Replaces the token at the specified position by the passed token.
void	setTokensAt(java.lang.String sequenceID, int beginIndex, java.util.Collection<? extends T> tokens) Replaces a sequence of tokens starting at the specified position.

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel

containsSequence, doAddSequence, doRemoveSequence, getSequenceCount, getSequenceMap, getSequenceOrder, sequenceIDIterator

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

addSequence, addSequence, appendToken, appendTokens, doRenameSequence, fireAfterSequenceChange, fireAfterTokenChange, getApproxMaxSequenceLength, getIDManager, getMaxSequenceLength, getTokenSet, isReuseSequenceIDs, isSequencesReadOnly, isTokensReadOnly, removeSequence, renameSequence, sequenceIDsByName, sequenceNameByID, setMaxSequeceLengthRecalculte, setReuseSequenceIDs, setTokenSet

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel

fireAfterSequenceRenamed, getChangeListeners, getID, getLabel, setID, setLabel

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_INITIAL_CAPACITY

public static final int DEFAULT_INITIAL_CAPACITY

See Also:

Constant Field Values

Constructor Detail

AbstractListAlignmentModel

public AbstractListAlignmentModel(TokenSet<T> tokenSet,
                                  SequenceIDManager idManager,
                                  boolean reuseSequenceIDs)

Creates a new instance of this class using DEFAULT_INITIAL_CAPACITY as the initial capacity which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.

Parameters:

tokenSet - the token set which is supported by the implementation

idManager - the ID manager to be used by the new instance (maybe shared among multiple instances)

reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure what this property does.)

AbstractListAlignmentModel

public AbstractListAlignmentModel(TokenSet<T> tokenSet,
                                  SequenceIDManager idManager,
                                  boolean reuseSequenceIDs,
                                  int initialCapacity,
                                  boolean useMaxLength)

Creates a new instance of this class.

Parameters:

tokenSet - the token set which is supported by the implementation

idManager - the ID manager to be used by the new instance (maybe shared among multiple instances)

reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model. (See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure what this property does.)

initialCapacity - the initial capacity newly generated array lists will have

useMaxLength - Specify true here if initialCapacity shall only be used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array lists.

Method Detail

getSequence

public java.util.List<T> getSequence(java.lang.String sequenceID)

getTokenAt

public T getTokenAt(java.lang.String sequenceID,
                    int index)

Description copied from interface: AlignmentModel

Returns the token at the specified position.

Parameters:

sequenceID - the identifier the sequence where the token is contained

index - the index of the element contained in the specified sequence (The first element has the index 0.)

Returns:

the token to be displayed in the GUI alignment view

setTokenAt

public void setTokenAt(java.lang.String sequenceID,
                       int index,
                       T token)
                throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Replaces the token at the specified position by the passed token.

Parameters:

sequenceID - the identifier the sequence where the token is contained

index - the index of the element to be replaced (The first element has the index 0.)

token - the new token for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

setTokensAt

public void setTokensAt(java.lang.String sequenceID,
                        int beginIndex,
                        java.util.Collection<? extends T> tokens)
                 throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Replaces a sequence of tokens starting at the specified position. If the specified collection contains more tokens than the currently present in the sequence at the specified start position the additional tokens are appended.

Parameters:

sequenceID - the identifier the sequence where the token is contained

beginIndex - the index of the first element to be replaced (The first element in the sequence has the index 0.)

tokens - the new tokens for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

See Also:

AlignmentModelUtils.charSequenceToTokenList(CharSequence, TokenSet)

insertTokenAt

public void insertTokenAt(java.lang.String sequenceID,
                          int index,
                          T token)
                   throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Inserts a token at the specified position. All tokens located behind the specified index are moved by 1.

Parameters:

sequenceID - the identifier the sequence in the alignment

index - the new index the inserted element will have (0 <= elementIndex < sequenceLength)

token - the token to be inserted

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

insertTokensAt

public void insertTokensAt(java.lang.String sequenceID,
                           int beginIndex,
                           java.util.Collection<? extends T> tokens)
                    throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Inserts a sequence of tokens starting at the specified position. All tokens located behind the specified index are moved by the number of tokens that are contained in tokens.

Parameters:

sequenceID - the identifier the sequence where the token is contained

beginIndex - the index of the first element to be replaced (The first element in the sequence has the index 0.)

tokens - the new tokens for the specified position

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

See Also:

AlignmentModelUtils.charSequenceToTokenList(CharSequence, TokenSet)

removeTokenAt

public void removeTokenAt(java.lang.String sequenceID,
                          int index)
                   throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Removes the token at the specified position from the underlying data source.

Parameters:

sequenceID - the identifier the sequence in the alignment

index - the index of the element to be removed (The first element has the index 0.)

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

removeTokensAt

public void removeTokensAt(java.lang.String sequenceID,
                           int beginIndex,
                           int endIndex)
                    throws AlignmentSourceNotWritableException

Description copied from interface: AlignmentModel

Removes the token inside the specified interval from the underlying data source. The subsequence to be removed begins at the specified beginIndex and extends to the token at index endIndex - 1). Thus the length of the subsequence is {@code endIndex - beginIndex}.

Parameters:

sequenceID - the identifier the sequence in the alignment

beginIndex - the beginning index, inclusive

endIndex - the ending index, exclusive

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens

getSequenceLength

public int getSequenceLength(java.lang.String sequenceID)

Description copied from interface: AlignmentModel

Returns the length of the specified sequence.

Parameters:

sequenceID - the identifier the sequence in the alignment

Returns:

the length of the sequence or -1 if no sequence with the specified name exists

getWriteType

public AlignmentModelWriteType getWriteType()

Description copied from interface: AlignmentModel

Returns a value that specifies if whole sequences or single tokens can be edited in the underlying data source. s

Returns:

the write type of this data source

getInitialCapacity

public int getInitialCapacity()

Returns the default initial capacity of new list objects created by #createNewSequence(int, String, int).

Returns:

the default initial capacity specified in the constructor

isUseMaxLength

public boolean isUseMaxLength()

Determines if the initial capacity of newly generated list objects shall only depend on the default capacity or also on the maximum length of the other lists already contained in this provider.

Returns:

true if new lists shall have the maximum length of all other lists already present in this provider if this maximum is higher than the return value of getInitialCapacity(), false if all new sequences shall always have an initial capacity of getInitialCapacity().

createNewSequence

protected abstract java.util.List<T> createNewSequence(java.lang.String sequenceID,
                                                       java.lang.String sequenceName,
                                                       int initialCapacity)

This method is called by #createNewSequence(int, String) and must be implemented by inherited classes. In contrast to #createNewSequence(int, String) it provides an additional parameter specifying the initial capacity the returned list object shall have. This parameter value if set depending on the return values of isUseMaxLength() either to a fixed value as specified by getInitialCapacity() or by the maximum length of other sequences in this provider if any of these contain more elements than getInitialCapacity().

Parameters:

sequenceID - the ID the new sequence must have

sequenceName - the name the new sequence will have

initialCapacity - the initial capacity the returned list object shall have

Returns:

the new sequence object

createNewSequence

protected java.util.List<T> createNewSequence(java.lang.String sequenceID,
                                              java.lang.String sequenceName)

Description copied from class: AbstractMapBasedAlignmentModel

Implementing classes must offer a way to create their custom instances of sequence objects overwriting this method. This method is called in #doAddSequence(int, String) before adding the new sequences to map and the oder list.

Specified by:

createNewSequence in class AbstractMapBasedAlignmentModel<java.util.List<T>,T>

Parameters:

sequenceID - the ID the new sequence must have

sequenceName - the name the new sequence will have

Returns:

the new sequence object